Hi Andrew just tested your xmls, using MartEditor from (.zip) distro available on our website DOCS
ftp://[EMAIL PROTECTED]/pub/software/biomart/martj_current/martj-bin.zip it works fine and creates datasets correctly. However the ERROR: "File does not contain valid configuration" is thrown when the connection to database doesnt support write access. could you please double check this and also try using the distro's martj-bin.zip if you are using a locally compiled batch file. may be this would give us some pointers. thanks syed On Wed, 2007-09-12 at 09:49 -0500, Vallejos, Andrew wrote: > Still doesn't work. > > I am using the mart-j tools for windows (not sure if that makes a > difference). > > -Andrew > > -----Original Message----- > From: Syed Haider [mailto:[EMAIL PROTECTED] > Sent: Wednesday, September 12, 2007 9:45 AM > To: Vallejos, Andrew > Cc: mart-dev > Subject: RE: [mart-dev] Duplicate Entry Error > > Hi Andrew > > attached are the two files you sent to me yesterday. > Just now, I have created a new database, using marteditor 0.6, I > connected to this new database, uploaded ('Upload All') the files by > selecting both simultaneously, then did 'import' and it works fine. > > could you please see if these two help you recover your work. > > cheers > syed > > > On Wed, 2007-09-12 at 09:15 -0500, Vallejos, Andrew wrote: > > I deleted it using the martEditor. > > > > I've tried loading both the single file and loading both the regular > > file and the *.template file together. > > > > -Andrew > > > > -----Original Message----- > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > Sent: Wednesday, September 12, 2007 9:11 AM > > To: Vallejos, Andrew > > Cc: mart-dev > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > to further diagnose this: > > - did you delete it using martEditor or you tried manual deletion from > > files ? > > > > - secondarily when you try to load xml from MartEditor, you need to > load > > *template.xml file, are you loading this one ? > > > > > > On Wed, 2007-09-12 at 09:06 -0500, Vallejos, Andrew wrote: > > > > > If so, then i would suggest to delete the existing filter which > is > > > > > causing you the trouble and redeclare it. hopefully that will > work > > > > > out. > > > > > > I deleted the existing filter list per your suggestion, and to save > > time > > > I saved a copy of the original xml and was going to load the saved > > copy > > > rather than recreate the filter list. > > > > > > -Andrew > > > > > > -----Original Message----- > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > Sent: Wednesday, September 12, 2007 9:04 AM > > > To: Vallejos, Andrew > > > Cc: mart-dev > > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > > > Hi Andrew > > > > > > On Wed, 2007-09-12 at 08:57 -0500, Vallejos, Andrew wrote: > > > > I cannot load my saved xml file(s). > > > > > > > > I get an error from the marteditor. > > > > > > > > "File does not contain valid configuration." > > > > > > thats not encouraging....this might be a problem with MartEditor. > > > Is there a chance that you do not need to reload your xmls and you > > just > > > connect to your database and do import. why do you have to use saved > > > xmls ? > > > > > > > > > > > > > > -Andrew > > > > > > > > -----Original Message----- > > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > Sent: Wednesday, September 12, 2007 8:47 AM > > > > To: Vallejos, Andrew > > > > Cc: mart-dev > > > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > > > > > > > > > > > > > On Wed, 2007-09-12 at 08:43 -0500, Vallejos, Andrew wrote: > > > > > perl bin/configure.pl --clean -r con/your_registry.xml --clean > > > > > > > > > > is the exact syntax that I use. Does it matter than the > '--clean' > > > is > > > > in > > > > > a different location? > > > > > > > > no, as long as its there, its fine. > > > > did you try removing existing filter and adding a new one ? > > > > > > > > cheers > > > > syed > > > > > > > > > > > > > > -Andrew > > > > > > > > > > > > > > > -----Original Message----- > > > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > > Sent: Wednesday, September 12, 2007 4:57 AM > > > > > To: Vallejos, Andrew; mart-dev > > > > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > > > > > > > Hi Andrew > > > > > Could you please confirm if once doing the 'export' from > > MartEditor, > > > > you > > > > > do reconfigure BioMart > > > > > > > > > > perl bin/configure.pl -r con/your_registry.xml --clean > > > > > > > > > > and kill/restart your server ? > > > > > > > > > > If so, then i would suggest to delete the existing filter which > is > > > > > causing you the trouble and redeclare it. hopefully that will > work > > > > out. > > > > > > > > > > cheers > > > > > syed > > > > > > > > > > > > > > > On Tue, 2007-09-11 at 13:52 -0500, Vallejos, Andrew wrote: > > > > > > Syed, > > > > > > > > > > > > Ok, so I am not getting the duplication error anymore. > However, > > I > > > > > have > > > > > > filters that are not showing up. > > > > > > > > > > > > The chromosome filter for gene map v3.4 and the disease > ontology > > > > > filters > > > > > > are not displaying on martview page. The chromosome I did get > > to > > > > > > display once, but then it disappeared the next time I updated > > the > > > > > file. > > > > > > > > > > > > -Andrew > > > > > > > > > > > > -----Original Message----- > > > > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > > > Sent: Friday, September 07, 2007 3:34 AM > > > > > > To: Vallejos, Andrew > > > > > > Cc: [email protected] > > > > > > Subject: Re: [mart-dev] Duplicate Entry Error > > > > > > > > > > > > Hi Andrew > > > > > > > > > > > > On Thu, 2007-09-06 at 15:44 -0500, Vallejos, Andrew wrote: > > > > > > > We've recently installed a test v0.6 mart. However, now > that > > I > > > am > > > > > > > using the v0.6 tools I keep receiving a "Remove Duplicates > > > before > > > > > > > generating Template" error. > > > > > > > > > > > > is it martEditor which throws this error ? If so, please send > me > > > > your > > > > > > xmls. I assume you get this error when you 'export'. Please > > > correct > > > > me > > > > > > if thats not the case. > > > > > > > > > > > > thanks > > > > > > syed > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I have no idea why I am getting this error as I have no > > > duplicates > > > > > in > > > > > > > my attribute tables, I've checked. > > > > > > > > > > > > > > > > > > > > > > > > > > > > -Andrew > > > > > > > > > > > > > > > > > > > > > > > > > > > > ====================== > > > > > > > > > > > > > > Andrew Vallejos > > > > > > > > > > > > > > Web Developer > > > > > > > > > > > > > > Medical College of Wisconsin > > > > > > > > > > > > > > 414-955-4104 > > > > > > > > > > > > > > [EMAIL PROTECTED] > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > ====================================== > > > Syed Haider. > > > EMBL-European Bioinformatics Institute > > > Wellcome Trust Genome Campus, Hinxton, > > > Cambridge CB10 1SD, UK. > > > ====================================== > > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
